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In recent years a variety of double and triple bonds between the semi-metallic elements have been reported, including silicon, germanium, arsenic, bismuth and so on. The ability of certain main group elements to catenate is currently the subject of research into inorganic polymers. | 0 | Organic Chemistry |
Although some metal oxides eventually release O2 when heated, these conversions generally require high temperatures. A few compounds release O2 at mild temperatures. Chemical oxygen generators consist of chemical compounds that release O when stimulated, usually by heat. They are used in submarines and commercial aircraft to provide emergency oxygen. Oxygen is generated by the high-temperature decomposition of sodium chlorate:
:2 NaClO → 2 NaCl + 3 O
Potassium permanganate also releases oxygen upon heating, but the yield is modest.
:2 KMnO → MnO + KMnO + O | 5 | Photochemistry |
A nitrogen bound to both a good electrofuge and a good nucleofuge is known as a nitrenoid (for its resemblance to a nitrene). Nitrenes lack a full octet of electrons are thus highly electrophilic; nitrenoids exhibit analogous behavior and are often good substrates for electrophilic amination reactions. Nitrenoids can be generated from O-alkylhydroxylamines containing an N−H bond via deprotonation or from O-alkyloximes via nucleophilic addition. These intermediates react with carbanions to give substituted amines. Other electron-deficient, sp amination reagents react by similar mechanisms to give substitution products.
In aminations involving oxaziridines, nucleophilic attack takes place on the nitrogen atom of the three-membered ring. For some substrates (α-cyano ketones, for example), the resulting alkoxide reacts further to afford unexpected products. Straightforward β-elimination of the alkoxide leads to the formation of an amine.
Additions across pi bonds appear to proceed by typical nucleophilic addition pathways in most cases. Alkyl-, aryl-, and heteroaryllithium reagents add to azides to afford triazene salts. Reduction of these salts leads to amines, although they also may be converted to azides upon acidic workup with overall elimination of sulfinic acid. | 0 | Organic Chemistry |
Flory and Stockmayer used a statistical approach to derive an expression to predict the gel point by calculating when approaches infinite size. The statistical approach assumes that (1) the reactivity of the functional groups of the same type is the same and independent of the molecular size and (2) there are no intramolecular reactions between the functional groups on the same molecule.
Consider the polymerization of bifunctional molecules , and multifunctional , where is the functionality. The extends of the functional groups are and , respectively. The ratio of all A groups, both reacted and unreacted, that are part of branched units, to the total number of A groups in the mixture is defined as . This will lead to the following reaction
The probability of obtaining the product of the reaction above is given by , since the probability that a B group reach with a branched unit is and the probability that a B group react with non-branched A is .
This relation yields to an expression for the extent of reaction of A functional groups at the gel point
where r is the ratio of all A groups to all B groups. If more than one type of multifunctional branch unit is present and average value is used for all monomer molecules with functionality greater than 2.
Note that the relation does not apply for reaction systems containing monofunctional reactants and/or both A and B type of branch units. | 7 | Physical Chemistry |
* Protein Data Bank (PDB): repository for protein sequence and structural information
* UniProt: provides sequence and functional information
* Structural Classification of Proteins (SCOP Classifications): hierarchical-based approach
* Class, Architecture, Topology and Homologous superfamily (CATH): hierarchical-based approach | 1 | Biochemistry |
Microscale thermophoresis (MST) measures the size, charge and hydration entropy of molecules/substrates at equilibrium. The thermophoretic movement of a fluorescently labeled substrate changes significantly as it is modified by an enzyme. This enzymatic activity can be measured with high time resolution in real time. The material consumption of the all optical MST method is very low, only 5 μl sample volume and 10nM enzyme concentration are needed to measure the enzymatic rate constants for activity and inhibition. MST allows analysts to measure the modification of two different substrates at once (multiplexing) if both substrates are labeled with different fluorophores. Thus substrate competition experiments can be performed. | 1 | Biochemistry |
From the ideal gas law PV = nRT we get:
where P is pressure, V is volume, n is number of moles of a given substance, and T is temperature.
As pressure is defined as force per area of measurement, the gas equation can also be written as:
Area and volume are (length) and (length) respectively. Therefore:
Since force × length = work:
The physical significance of R is work per mole per degree. It may be expressed in any set of units representing work or energy (such as joules), units representing degrees of temperature on an absolute scale (such as kelvin or rankine), and any system of units designating a mole or a similar pure number that allows an equation of macroscopic mass and fundamental particle numbers in a system, such as an ideal gas (see Avogadro constant).
Instead of a mole the constant can be expressed by considering the normal cubic meter.
Otherwise, we can also say that:
Therefore, we can write R as:
And so, in terms of SI base units:
:R = . | 7 | Physical Chemistry |
Two methods are used to assign raw sequence reads to genomic features (i.e., assemble the transcriptome):
* De novo: This approach does not require a reference genome to reconstruct the transcriptome, and is typically used if the genome is unknown, incomplete, or substantially altered compared to the reference. Challenges when using short reads for de novo assembly include 1) determining which reads should be joined together into contiguous sequences (contigs), 2) robustness to sequencing errors and other artifacts, and 3) computational efficiency. The primary algorithm used for de novo assembly transitioned from overlap graphs, which identify all pair-wise overlaps between reads, to de Bruijn graphs, which break reads into sequences of length k and collapse all k-mers into a hash table. Overlap graphs were used with Sanger sequencing, but do not scale well to the millions of reads generated with RNA-Seq. Examples of assemblers that use de Bruijn graphs are Trinity, Oases (derived from the genome assembler Velvet), Bridger, and rnaSPAdes. Paired-end and long-read sequencing of the same sample can mitigate the deficits in short read sequencing by serving as a template or skeleton. Metrics to assess the quality of a de novo assembly include median contig length, number of contigs and N50.
* Genome guided: This approach relies on the same methods used for DNA alignment, with the additional complexity of aligning reads that cover non-continuous portions of the reference genome. These non-continuous reads are the result of sequencing spliced transcripts (see figure). Typically, alignment algorithms have two steps: 1) align short portions of the read (i.e., seed the genome), and 2) use dynamic programming to find an optimal alignment, sometimes in combination with known annotations. Software tools that use genome-guided alignment include Bowtie, TopHat (which builds on BowTie results to align splice junctions), Subread, STAR, HISAT2, and GMAP. The output of genome guided alignment (mapping) tools can be further used by tools such as Cufflinks or StringTie to reconstruct contiguous transcript sequences (i.e., a FASTA file). The quality of a genome guided assembly can be measured with both 1) de novo assembly metrics (e.g., N50) and 2) comparisons to known transcript, splice junction, genome, and protein sequences using precision, recall, or their combination (e.g., F1 score). In addition, in silico assessment could be performed using simulated reads.
A note on assembly quality: The current consensus is that 1) assembly quality can vary depending on which metric is used, 2) assembly tools that scored well in one species do not necessarily perform well in the other species, and 3) combining different approaches might be the most reliable. | 1 | Biochemistry |
Engineering diffraction refers to a sub-field of neutron scattering which investigates microstructural features that influence the mechanical properties of materials. These include:
#lattice strain, a measure of distortion in crystals
#texture, a measure of grain orientations
#dislocation density, a measure of the microstructure
#grain morphology | 7 | Physical Chemistry |
A backdraft can occur when a compartment fire has little or no ventilation. Due to this, little or no oxygen can flow into the compartment. Then, because fires reduce oxygen, the oxygen concentration decreases. When the oxygen concentration becomes too low to support combustion, some or all of the combustion switches to pyrolysis. However, the hydrocarbons and smoke (primarily particulate matter) remain at a temperature hot enough to auto-ignite. If oxygen is then re-introduced to the compartment, e.g. by opening a door or window to a closed room, while the gasses are still hot enough to auto-ignite, combustion will restart, often abruptly or even explosively, as the gasses are heated by the combustion and expand rapidly because of the rapidly increasing temperature, combined with the energy released from combustion.
The colour and movement of smoke is used by firefighters to infer fire conditions, including the risk of backdraft. Characteristic warning signs of a backdraft include yellow or brown smoke, smoke which exits small holes in puffs (a sort of breathing effect) and is often found around the edges of doors and windows, and windows which appear brown or black when viewed from the exterior due to soot from incomplete combustion. This is an indication that the room lacks enough oxygen to permit oxidation of the soot particles. Firefighters often look to see if there is soot on the inside of windows and in any cracks in the window (caused e.g. by the heat). The windows may also have a slight vibration due to varying pressure within the compartment due to intermittent combustion.
If firefighters discover a room sucking air into itself, for example through a crack, they generally evacuate immediately, because this is a strong indication that a backdraft is imminent. Due to pressure differences, puffs of smoke are sometimes drawn back into the enclosed space from which they emanated, which is how the term backdraft originated.
Backdrafts are very dangerous, often surprising even experienced firefighters. The most common tactic used by firefighters to defuse a potential backdraft is to ventilate a room from its highest point, allowing the heat and smoke to escape without igniting.
Common signs of imminent backdraft include a sudden inrush of air upon an opening into a compartment being created, lack of visible signs of flame (fire above its upper flammability limit), "pulsing" smoke plumes from openings and auto-ignition of hot gases at openings where they mix with oxygen in the surrounding air. | 7 | Physical Chemistry |
Superfluid vacuum theory (SVT) is an approach in theoretical physics and quantum mechanics where the physical vacuum is viewed as superfluid.
The ultimate goal of the approach is to develop scientific models that unify quantum mechanics (describing three of the four known fundamental interactions) with gravity. This makes SVT a candidate for the theory of quantum gravity and an extension of the Standard Model.
It is hoped that development of such a theory would unify into a single consistent model of all fundamental interactions,
and to describe all known interactions and elementary particles as different manifestations of the same entity, superfluid vacuum.
On the macro-scale a larger similar phenomenon has been suggested as happening in the murmurations of starlings. The rapidity of change in flight patterns mimics the phase change leading to superfluidity in some liquid states.
Light behaves like a superfluid in various applications such as Poisson's Spot. As the liquid helium shown above, light will travel along the surface of an obstacle before continuing along its trajectory. Since light is not affected by local gravity its "level" becomes its own trajectory and velocity. Another example is how a beam of light travels through the hole of an aperture and along its backside before diffraction. | 7 | Physical Chemistry |
Dissolved organic matter (DOM) is one of the most active and mobile carbon pools and has an important role in global carbon cycling. In addition, dissolved organic carbon (DOC) affects the soil negative electrical charges denitrification process, acid-base reactions in the soil solution, retention and translocation of nutrients (cations), and immobilization of heavy metals and xenobiotics. Soil DOM can be derived from different sources (inputs), such as atmospheric carbon dissolved in rainfall, litter and crop residues, manure, root exudates, and decomposition of soil organic matter (SOM). In the soil, DOM availability depends on its interactions with mineral components (e.g., clays, Fe and Al oxides) modulated by adsorption and desorption processes. It also depends on SOM fractions (e.g., stabilized organic molecules and microbial biomass) by mineralization and immobilization processes. In addition, the intensity of these interactions changes according to soil inherent properties, land use, and crop management.
During the decomposition of organic material, most carbon is lost as CO to the atmosphere by microbial oxidation. Soil type and landscape slope, leaching, and runoff are also important processes associated to DOM losses in the soil. In well-drained soils, leached DOC can reach the water table and release nutrients and pollutants that can contaminate groundwater, whereas runoff transports DOM and xenobiotics to other areas, rivers, and lakes. | 2 | Environmental Chemistry |
In June 2010, the first case report appeared of a progressive multifocal leukoencephalopathy being successfully treated with mefloquine. Mefloquine can also act against the JC virus. Administration of mefloquine seemed to eliminate the virus from the patient's body and prevented further neurological deterioration.
Mefloquine alters cholinergic synaptic transmission through both postsynaptic and presynaptic actions. The postsynaptic action to inhibit acetylcholinesterase changes transmission across synapses in the brain. | 4 | Stereochemistry |
The two main tasks of transcription initiation are to provide RNA polymerase with an access to the promoter and to assemble general transcription factors with polymerase into a transcription initiation complex. Diverse mechanisms of initiating transcription by overriding inhibitory signals at the gene promoter have been identified. Eukaryotic genes have acquired extensive regulatory sequences that encompass a large number of regulator-binding sites and spread overall kilobases (sometimes hundreds of kilobases) from the promoter–-both upstream and downstream. The regulator binding sites are often clustered together into units called enhancers. Enhancers can facilitate highly cooperative action of several transcription factors (which constitute enhanceosomes). Remote enhancers allow transcription regulation at a distance. Insulators situated between enhancers and promoters help define the genes that an enhancer can or cannot influence.
Eukaryotic transcriptional activators have separate DNA-binding and activating functions. Upon binding to its cis-element, an activator can recruit polymerase directly or recruit other factors needed by the transcriptional machinery. An activator can also recruit nucleosome modifiers that alter chromatin in the vicinity of the promoter and thereby help initiation. Multiple activators can work together, either by recruiting a common or two mutually dependent components of the transcriptional machinery, or by helping each other bind to their DNA sites. These interactions can synergize multiple signaling inputs and produce intricate transcriptional responses to address cellular needs. | 1 | Biochemistry |
Methanesulfonyl chloride is mainly used to give methanesulfonates by its reaction with alcohols in the presence of a non-nucleophilic base. In contrast to the formation of toluenesulfonates from alcohols and p-toluenesulfonyl chloride in the presence of pyridine, the formation of methanesulfonates is believed to proceed via a mechanism wherein methanesulfonyl chloride first undergoes an E1cb elimination to generate the highly reactive parent sulfene (), followed by attack by the alcohol and rapid proton transfer to generate the observed product. This mechanistic proposal is supported by isotope labeling experiments and the trapping of the transient sulfene as cycloadducts.
Methanesulfonates are used as intermediates in substitution reactions, elimination reactions, reductions, and rearrangement reactions. When treated with a Lewis acid, oxime methanesulfonates undergo facile Beckmann rearrangement.
Methanesulfonates are occasionally used as a protecting group for alcohols. They are stable to acidic conditions and is cleaved back to the alcohol using sodium amalgam. | 0 | Organic Chemistry |
Initially, the chemical reactions that normally occur in the cement paste, generate an alkaline environment, bringing the solution in the cement paste pores to pH values around 13. In these conditions, passivation of steel rebar occurs, due to a spontaneous generation of a thin film of oxides able to protect the steel from corrosion. Over time, the thin film can be damaged, and corrosion of steel rebar starts. The corrosion of steel rebar is one of the main causes of premature failure of reinforced concrete structures worldwide, mainly as a consequence of two degradation processes, carbonation and penetration of chlorides. With regard to the corrosion degradation process, a simple and accredited model for the assessment of the service life is the one proposed by Tuutti, in 1982. According to this model, the service life of a reinforced concrete structure can be divided into two distinct phases.
* , initiation time: from the moment the structure is built, to the moment corrosion initiates on steel rebar. More in particular, it is the time required for aggressive agents (carbon dioxide and chlorides) to penetrate the concrete cover thickness, reach the embedded steel rebar, alter the initial passivation condition on steel surface and cause corrosion initiation.
* , propagation time: which is defined as the time from the onset of active corrosion until an ultimate limit state is reached, i.e. corrosion propagation reaches a limit value corresponding to unacceptable structural damage, such as cracking and detachment of the concrete cover thickness.
The identification of initiation time and propagation time is useful to further identify the main variables and processes influencing the service life of the structure which are specific of each service life phase and of the degradation process considered. | 8 | Metallurgy |
Chibale grew up without electricity or running water in Muwele Village, Chief Chiundaponde, Mpika district, Zambia. His parents are Elizabeth Malekano Chanda and Harrison Chibale. He studied chemistry at the University of Zambia, graduating in 1987. Chibale worked at Kafironda Explosives in Mufulira. As there were no opportunities for graduate studies in Zambia, he moved to the University of Cambridge for his PhD, working in Stuart Warren's group on synthetic organic chemistry of optically active molecules. He was funded by a Cambridge Livingstone Trust scholarship. | 0 | Organic Chemistry |
Ketenimines are a group of organic compounds sharing a common functional group with the general structure RRC=C=NR. A ketenimine is a cumulated alkene and imine and is related to an allene and a ketene.
The parent compound is ketenimine or CHCNH. The most recent work by Bane et al. investigates the rovibrational structure of the ν and ν bands in the high-resolution FTIR spectrum, complementing the earlier analysis of the pure rotational spectrum. This pair of Coriolis coupled bands provide a rare example where intensity sharing between bands yields sufficient intensity for an otherwise invisible band (ν). | 0 | Organic Chemistry |
*King G.R., Mander L.N., Monck N.J.T., Morris J.C. and Zhang H. A New and Efficient Strategy for the Total Synthesis of Polycyclic Diterpenoids: The Preparation of Gibberellins (±)-GA103 and (±)-GA73. J. Am. Chem. Soc. 1997, 119, 3828–3829.
*Frey, B., Wells, A. P., Rogers, D. R. and Mander, L. N. Synthesis of the Unusual Diterpenoid Tropones, Hainanolidol and Harringtonolide. J. Am. Chem. Soc. 1998, 120, 1914–1915.
*Mander, L. N. Twenty years of gibberellin research. Natural Product Reports, 2003, 20, 49–69.
*Mander, L. N. and McLachlan, M. M. Total synthesis of the Galbulimima alkaloid GB 13. J. Am. Chem. Soc., 2003, 125, 2400–2401.
*Mander, L. N. and Thomson, R. J. Total synthesis of Sordaricin. Org. Lett., 2003, 5, 1321–1324. | 0 | Organic Chemistry |
The presence or absence of certain plant or other vegetative life in an ecosystem can provide important clues about the health of the environment: environmental preservation. There are several types of plant biomonitors, including mosses, lichens, tree bark, bark pockets, tree rings, and leaves. As an example, environmental pollutants can be absorbed and incorporated into tree bark, which can then be analyzed to pollutant presence and concentration in the surrounding environment. The leaves of certain vascular plants experience harmful effects in the presence of ozone, particularly tissue damage, making them useful in detecting the pollutant. These plants are observed abundantly in Atlantic islands in the Northern Hemisphere, the Mediterranean Basin, equatorial Africa, Ethiopia, the Indian coastline, the Himalayan region, southern Asia, and Japan. These regions with high endemic richness are particularly vulnerable to ozone pollution, emphasizing the importance of certain vascular plant species as valuable indicators of environmental health in terrestrial ecosystems. Conservationists use such plant bioindicators as tools, allowing them to ascertain potential changes and damages to the environment.
As an example, Lobaria pulmonaria has been identified as an indicator species for assessing stand age and macrolichen diversity in Interior Cedar–Hemlock forests of east-central British Columbia, highlighting its ecological significance as a bioindicator. The abundance of Lobaria pulmonaria was strongly correlated with this increase in diversity, suggesting its potential as an indicator of stand age in the ICH. Another Lichen species, Xanthoria parietina, serves as a reliable indicator of air quality, effectively accumulating pollutants like heavy metals and organic compounds. Studies have shown that X. parietina samples collected from industrial areas exhibit significantly higher concentrations of these pollutants compared to those from greener, less urbanized environments. This highlights the lichen's valuable role in assessing environmental health and identifying areas with elevated pollution levels, aiding in targeted mitigation efforts and environmental management strategies.
Fungi is also useful as bioindicators, as they are found throughout the globe and undergo noticeable changes in different environments.
Lichens are organisms comprising both fungi and algae. They are found on rocks and tree trunks, and they respond to environmental changes in forests, including changes in forest structure – conservation biology, air quality, and climate. The disappearance of lichens in a forest may indicate environmental stresses, such as high levels of sulfur dioxide, sulfur-based pollutants, and nitrogen oxides.
The composition and total biomass of algal species in aquatic systems serve as an important metric for organic water pollution and nutrient loading such as nitrogen and phosphorus.
There are genetically engineered organisms that can respond to toxicity levels in the environment; e.g., a type of genetically engineered grass that grows a different colour if there are toxins in the soil. | 2 | Environmental Chemistry |
Aptamers have emerged as a novel category in the field of bioreceptors due to their wide applications ranging from biosensing to therapeutics. Several variations of their screening process, called SELEX have been reported which can yield sequences with desired properties needed for their final use. | 1 | Biochemistry |
Uzer has more than 80 referenced Journal articles, in a number of highly respected scientific journals.
* [http://link.aps.org/abstract/PRE/v48/p3414 appeared in PRE] Chaotic billiards with neutral boundaries
* [http://www.sciencemag.org/cgi/content/abstract/253/5015/42 appeared in Science] Celestial Mechanics on a Microscopic Scale
* [http://link.aip.org/link/?JCPSA6/81/5013/1 appeared in JCP] Quantization with operators appropriate to shapes of trajectories and classical perturbation theory | 7 | Physical Chemistry |
In New Haven, the decommissioned English Station has a high concentration of PCB contamination due to the chemicals used in the running of the plant. This, along with asbestos contamination, has made cleaning and demolishing the abandoned site extremely difficult. The PCB contamination has spread to the soil, and to the river, where locals will sometimes fish unaware of the danger. | 2 | Environmental Chemistry |
If the thickness of the diffusion layer is known, the finite-length Warburg element is defined as:
where
where is the thickness of the diffusion layer and is the diffusion coefficient.
There are two special conditions of finite-length Warburg elements: the Warburg Short () for a transmissive boundary, and the Warburg Open () for a reflective boundary. | 7 | Physical Chemistry |
* Phosphofructokinase 1 catalyzes the first committed step of glycolysis.
* LpxC catalyzes the first committed step of lipid A biosynthesis.
* 8-amino-7-oxononanoate synthase catalyzes the first committed step in plant biotin synthesis.
* MurA catalyzes the first committed step of peptidoglycan biosynthesis.
*Aspartate transcarbamoylase catalyzes the committed step in the pyrimidine biosynthetic pathway in E. coli.
*3-deoxy-D-arabinose-heptulsonate 7-phosphate synthase catalyses the first committed step of the shikimate pathway responsible for the synthesis of the aromatic amino acids Tyrosine, Tryptophan and Phenylalanine in plants, bacteria, fungi and some lower eukaryotes.
*Citrate synthase catalyzes the addition of acetyl-CoA to oxaloacetate and is the first committed step of the Citric Acid Cycle.
*Acetyl-CoA carboxylase catalyzes the irreversible carboxylation of acetyl-CoA to malonyl-CoA in the first committed step of fatty acid biosynthesis.
*Glucose-6-phosphate dehydrogenase catalyzes the conversion of G6P into 6-phosphogluconolactone to produce NADPH in the first and committed step of the pentose phosphate pathway. | 1 | Biochemistry |
The PMF can be obtained in Monte Carlo or molecular dynamics simulations to examine how a systems energy changes as a function of some specific reaction coordinate parameter. For example, it may examine how the systems energy changes as a function of the distance between two residues, or as a protein is pulled through a lipid bilayer. It can be a geometrical coordinate or a more general energetic (solvent) coordinate. Often PMF simulations are used in conjunction with umbrella sampling, because typically the PMF simulation will fail to adequately sample the system space as it proceeds. | 7 | Physical Chemistry |
Conjugated azomethine ylides are capable of [1,5]- and [1,7]-electrocyclizations. An example of a [1,7]-electrocyclization of a azomethine ylide is shown below. This conrotatory ring-closing is followed by a suprafacial [1,5]-hydride shift, which affords the rearomatized product. The sterics and geometry of the reacting phenyl ring play a major role in the success of the reaction.
The compounds resulting from this type of electrocyclization have been used as dienes in Diels–Alder reactions to attach compounds to fullerenes. | 0 | Organic Chemistry |
When pressure approaches zero, all real gas will behave like ideal gas, that is, of a mole of gas relying only on temperature. Therefore, we can design a scale with as its argument. Of course any bijective function will do, but for convenience's sake a linear function is the best. Therefore, we define it as
The ideal gas scale is in some sense a "mixed" scale. It relies on the universal properties of gas, a big advance from just a particular substance. But still it is empirical since it puts gas at a special position and thus has limited applicability—at some point no gas can exist. One distinguishing characteristic of ideal gas scale, however, is that it precisely equals thermodynamical scale when it is well defined (see ). | 7 | Physical Chemistry |
Chromatography is a common technique used in the field of Forensic Science. Chromatography is a method of separating the components of a mixture from a mobile phase. Chromatography is an essential tool used in forensic science, helping analysts identify and compare trace amounts of samples including ignitable liquids, drugs, and biological samples. Many laboratories utilize gas chromatography/mass spectrometry (GC/MS) to examine these kinds of samples; this analysis provides rapid and reliant data to identify samples in question. | 3 | Analytical Chemistry |
In physics, deflection is a change in a moving object's velocity, hence its trajectory, as a consequence of contact (collision) with a surface or the influence of a non-contact force field. Examples of the former include a ball bouncing off the ground or a bat; examples of the latter include a beam of electrons used to produce a picture, or the relativistic bending of light due to gravity. | 7 | Physical Chemistry |
In the IUPAC Nomenclature system, ethers are named using the general formula "alkoxyalkane", for example CH–CH–O–CH is methoxyethane. If the ether is part of a more-complex molecule, it is described as an alkoxy substituent, so –OCH would be considered a "methoxy-" group. The simpler alkyl radical is written in front, so CH–O–CHCH would be given as methoxy(CHO)ethane(CHCH). | 0 | Organic Chemistry |
Remnants of L2 and L3 elements are found in the human genome. It is estimated that L2 and L3 elements were active ~200-300 million years ago. Due to the age of L2 elements found within therian genomes, they lack flanking target site duplications. The L2 (and L3) elements are in the same group as the CR1 clade, Jockey. | 1 | Biochemistry |
All commonly used cloning vectors in molecular biology have key features necessary for their function, such as a suitable cloning site and selectable marker. Others may have additional features specific to their use. For reason of ease and convenience, cloning is often performed using E. coli. Thus, the cloning vectors used often have elements necessary for their propagation and maintenance in E. coli, such as a functional origin of replication (ori). The ColE1 origin of replication is found in many plasmids. Some vectors also include elements that allow them to be maintained in another organism in addition to E. coli, and these vectors are called shuttle vector. | 1 | Biochemistry |
Grain boundaries are the preferential site for segregation of impurities, which may form a thin layer with a different composition from the bulk and a variety of atomic structures that are distinct from the abutting crystalline phases. For example, a thin layer of silica, which also contains impurity cations, is often present in silicon nitride.
Grain boundary complexions were introduced by Ming Tang, Rowland Cannon, and W. Craig Carter in 2006.
These grain boundary phases are thermodynamically stable and can be considered as quasi-two-dimensional phase, which may undergo to transition, similar to those of bulk phases. In this case structure and chemistry abrupt changes are possible at a critical value of a thermodynamic parameter like temperature or pressure. This may strongly affect the macroscopic properties of the material, for example the electrical resistance or creep rates. Grain boundaries can be analyzed using equilibrium thermodynamics but cannot be considered as phases, because they do not satisfy Gibbs'definition: they are inhomogeneous, may have a gradient of structure, composition or properties. For this reasons they are defined as complexion: an interfacial material or stata that is in thermodynamic equilibrium with its abutting phases, with a finite and stable thickness (that is typically 2–20 Å). A complexion need the abutting phase to exist and its composition and structure need to be different from the abutting phase. Contrary to bulk phases, complexions also depend on the abutting phase. For example, silica rich amorphous layer present in SiN, is about 10 Å thick, but for special boundaries this equilibrium thickness is zero. Complexion can be grouped in 6 categories, according to their thickness: monolayer, bilayer, trilayer, nanolayer (with equilibrium thickness between 1 and 2 nm) and wetting. In the first cases the thickness of the layer will be constant; if extra material is present it will segregate at multiple grain junction, while in the last case there is no equilibrium thickness and this is determined by the amount of secondary phase present in the material. One example of grain boundary complexion transition is the passage from dry boundary to biltilayer in Au-doped Si, which is produced by the increase of Au. | 8 | Metallurgy |
Phosphorus tribromide, like PCl and PF, has both properties of a Lewis base and a Lewis acid. For example, with a Lewis acid such as boron tribromide it forms stable 1 :1 adducts such as BrB · PBr. At the same time PBr can react as an electrophile or Lewis acid in many of its reactions, for example with amines.
An important reaction of PBr is with alcohols, where it replaces an OH group with a bromine atom to produce an alkyl bromide. All three bromides can be transferred.
Several detailed procedures are available. In some cases, triphenylphosphine/Br is superior to PBr.
The mechanism for a primary alcohol involves formation of a phosphorous ester (to form a good leaving group), followed by an S2 substitution.
Because of the S2 substitution step, the reaction generally works well for primary and secondary alcohols, but fails for tertiary alcohols. If the reacting carbon centre is chiral, the reaction usually occurs with inversion of configuration at the carbon alpha to the alcohol, as is usual with an S2 reaction.
In a similar reaction, PBr also converts carboxylic acids to acyl bromides: | 0 | Organic Chemistry |
Temperature-programmed reduction is a technique for the characterization of solid materials and is often used in the field of heterogeneous catalysis to find the most efficient reduction conditions, an oxidized catalyst precursor is submitted to a programmed temperature rise while a reducing gas mixture is flowed over it. It was developed by John Ward Jenkins whilst developing heterogeneous catalysts for Shell Oil company, but was never patented. | 7 | Physical Chemistry |
During the development of the vertebrate nervous system, many neurons become redundant (because they have died, failed to connect to target cells, etc.) and are eliminated. At the same time, developing neurons send out axon outgrowths that contact their target cells. Such cells control their degree of innervation (the number of axon connections) by the secretion of various specific neurotrophic factors that are essential for neuron survival. One of these is nerve growth factor (NGF or beta-NGF), a vertebrate protein that stimulates division and differentiation of sympathetic and embryonic sensory neurons. NGF is mostly found outside the central nervous system (CNS), but slight traces have been detected in adult CNS tissues, although a physiological role for this is unknown. It has also been found in several snake venoms.
In the peripheral and central neurons, neurotrophins are important regulators for survival, differentiation, and maintenance of nerve cells. They are small proteins that secrete into the nervous system to help keep nerve cells alive. There are two distinct classes of glycosylated receptors that can bind to neurotrophins. These two proteins are p75 (NTR), which binds to all neurotrophins, and subtypes of Trk, which are each specific for different neurotrophins. The reported structure above is a 2.6 Å-resolution crystal structure of neurotrophin-3 (NT-3) complexed to the ectodomain of glycosylated p75 (NRT), forming a symmetrical crystal structure. | 1 | Biochemistry |
Ampicillin is used to treat infections by many gram-positive and gram-negative bacteria. It was the first "broad spectrum" penicillin with activity against gram-positive bacteria, including Streptococcus pneumoniae, Streptococcus pyogenes, some isolates of Staphylococcus aureus (but not penicillin-resistant or methicillin-resistant strains), Trueperella, and some Enterococcus. It is one of the few antibiotics that works against multidrug resistant Enterococcus faecalis and E. faecium. Activity against gram-negative bacteria includes Neisseria meningitidis, some Haemophilus influenzae, and some of the Enterobacteriaceae (though most Enterobacteriaceae and Pseudomonas are resistant). Its spectrum of activity is enhanced by co-administration of sulbactam, a drug that inhibits beta lactamase, an enzyme produced by bacteria to inactivate ampicillin and related antibiotics. It is sometimes used in combination with other antibiotics that have different mechanisms of action, like vancomycin, linezolid, daptomycin, and tigecycline. | 4 | Stereochemistry |
It is not necessary that the embryo transfer be performed on the female who provided the eggs. Thus another female whose uterus is appropriately prepared can receive the embryo and become pregnant.
Embryo transfer may be used where a woman who has eggs but no uterus and wants to have a biological baby; she would require the help of a gestational carrier or surrogate to carry the pregnancy. Also, a woman who has no eggs but a uterus may utilize egg donor IVF, in which case another woman would provide eggs for fertilization and the resulting embryos are placed into the uterus of the patient. Fertilization may be performed using the womans partners sperm or by using donor sperm. Spare embryos which are created for another couple undergoing IVF treatment but which are then surplus to that couples needs may also be transferred (called embryo donation). Embryos may be specifically created by using eggs and sperm from donors and these can then be transferred into the uterus of another woman. A surrogate may carry a baby produced by embryo transfer for another couple, even though neither she nor the commissioning' couple is biologically related to the child. Third party reproduction is controversial and regulated in many countries. Persons entering gestational surrogacy arrangements must make sense of an entirely new type of relationship that does not fit any of the traditional scripts we use to categorize relations as kinship, friendship, romantic partnership or market relations. Surrogates have the experience of carrying a baby that they conceptualize as not of their own kin, while intended mothers have the experience of waiting through nine months of pregnancy and transitioning to motherhood from outside of the pregnant body. This can lead to new conceptualizations of body and self. | 1 | Biochemistry |
This book describes smelting, which Agricola describes as perfecting the metal by fire. The design of furnaces is first explained.
These are very similar for smelting different metals, constructed of brick or soft stone with a brick front and mechanically driven bellows at the rear. At the front is a pit called the fore-hearth to receive the metal. The furnace is charged with beneficiated ore and crushed charcoal and lit. In some gold and silver smelting a lot of slag is produced because of the relative poverty of the ore and the tap hole has to be opened at various times to remove different slag materials. When the furnace is ready, the forehearth is filled with molten lead into which the furnace is tapped. In other furnaces the smelting can be continuous, and lead is placed into the furnace if there is none in the ore. The slag is skimmed off the top of the metal as it is tapped. The lead containing the gold is separated by cupellation, the metal rich slags are re-smelted. Other smelting processes are similar, but lead is not added. Agricola also describes making crucible steel and distilling mercury and bismuth in this book. | 8 | Metallurgy |
Calmodulin is a small, highly conserved protein that is 148 amino acids long (16.7 kDa). The protein has two approximately symmetrical globular domains (the N- and C- domains) each containing a pair of EF hand motifs separated by a flexible linker region for a total of four Ca binding sites, two in each globular domain. In the Ca-free state, the helices that form the four EF-hands are collapsed in a compact orientation, and the central linker is disordered; in the Ca-saturated state, the EF-hand helices adopt an open orientation roughly perpendicular to one another, and the central linker forms an extended alpha-helix in the crystal structure, but remains largely disordered in solution. The C-domain has a higher binding affinity for Ca than the N-domain.
Calmodulin is structurally quite similar to troponin C, another Ca-binding protein containing four EF-hand motifs. However, troponin C contains an additional alpha-helix at its N-terminus, and is constitutively bound to its target, troponin I. It therefore does not exhibit the same diversity of target recognition as does calmodulin. | 1 | Biochemistry |
Tuck-in complexes retain nucleophilicity at the methylene carbon. They can be activated by Lewis acids to generate active catalysts for use in Ziegler–Natta catalysis. The Lewis acid attaches to the CH group, exposing a vacant site on the electrophilic Zr(IV) centre. | 0 | Organic Chemistry |
Sharpless was born April 28, 1941, in Philadelphia, Pennsylvania. His childhood was filled with summers at his family cottage on the Manasquan River in New Jersey. This is where Sharpless developed a love for fishing that he would continue throughout his life, spending summers in college working on fishing boats. He graduated from Friends Central School in 1959, and continued his studies at Dartmouth College, earning an A.B. in 1963. Sharpless originally planned to attend medical school after his undergraduate degree, but his research professor convinced him to continue his education in chemistry. He earned his Ph.D. in Organic Chemistry from Stanford University in 1968 under Eugene van Tamelen. He continued post-doctoral work at Stanford University (1968–1969) with James P. Collman, working on organometallic chemistry. Sharpless then moved to Harvard University (1969–1970), studying enzymology in Konrad E. Blochs lab. | 4 | Stereochemistry |
Many glycan binding proteins (GBPs) are oligomeric and typically contain multiple sites for glycan binding (also called carbohydrate-recognition domains). The ability to form multivalent protein-ligand interactions significantly enhances the strength of binding: while values for individual CRD-glycan interactions may be in the mM range, the overall affinity of GBP towards glycans may reach nanomolar or even picomolar ranges. The overall strength of interactions is described as avidity (in contrast with an affinity which describes single equilibrium). Sometimes the avidity is also called an apparent to emphasize the non-equilibrium nature of the interaction.
Common oligomerization structures of lectins are shown below. For example, galectins are usually observed as dimers, while intelectins form trimers and pentraxins assemble into pentamers. Larger structures, like hexameric Reg proteins, may assemble into membrane penetrating pores. Collectins may form even more bizarre complexes: bouquets of trimers or even cruciform-like structures (e.g. in SP-D). | 1 | Biochemistry |
There is one particular reaction studied by Grutzmacher et al. that exhibits the rearrangement of coordination character of PCO. Initially when reacting the anion with triorganyl silicon compounds, it binds via the oxygen forming the kinetic oxyphosphaalkyne product. The thermodynamic silyl phosphaketene product is generated when the kinetic product rearranges to allow PCO to coordinate through phosphorus.
The formation of the kinetic product is charged controlled and thus explains why it is formed by oxygen coordination. The oxygen atom favours a larger degree of ionic interactions as a result of its greater electronegativity. Contrastingly, the thermodynamic product of the reaction is generated under orbital control. This comes in the form of phosphorus coordination as the largest contribution in the HOMO of the anion resides on the phosphorus atom; this is clearly visible in Figure 3. | 7 | Physical Chemistry |
A cyclone sampler consists of a circular chamber with the aerosol stream entering through one or more tangential nozzles. Like an impactor, a cyclone sampler depends upon the inertia of the particle to cause it to deposit on the sampler wall as the air stream curves around inside the chamber. Also like an impactor, the collection efficiency depends upon the flow rate. Cyclones are less prone to particle bounce than impactors and can collect larger quantities of material. They also may provide a more gentle collection than impactors, which can improve the recovery of viable microorganisms. However, cyclones tend to have collection efficiency curves that are less sharp than impactors, and it is simpler to design a compact cascade impactor compared to a cascade of cyclone samplers. | 7 | Physical Chemistry |
Metabolomics can be applied to oncometabolism, since the changes in cancer's genomic, transcriptomic, and proteomic profiles can result in changes in downstream metabolic pathways. With this information we can elucidate the responsible pathways and oncometabolites for various diseases. Actually, through the use of this technique, the dysregulation of the pyruvate kinase enzyme in glucose metabolism was discovered in cancer cells. Another common used technique is glucose or glutamine labeled with 13C to show that the TCA cycle is used to generate large amounts of fatty acids (phospholipids) and to replenish the TCA cycle intermediates. But oncometabolomics does not necessarily need to be used on cancer cells, but on cells immediately surrounding them in the TME.
Metabolomics applied to cancer has the potential to significantly improve current oncological treatments and has a great diagnostic value, since metabolic changes are the prequel of phenotypic changes in cells (thus tissues and organs) making it suitable for early detection of difficult-to-detect cancers. This also leads to a more personalized medicine and customize an individual's cancer treatment according to their specific oncometabolite profiles, which would allow for better cancer therapy customization or informed adjustments. | 1 | Biochemistry |
Azlocillin is an acyl ampicillin antibiotic with an extended spectrum of activity and greater in vitro potency than the carboxy penicillins.
Azlocillin is similar to mezlocillin and piperacillin. It demonstrates antibacterial activity against a broad spectrum of bacteria, including Pseudomonas aeruginosa and, in contrast to most cephalosporins, exhibits activity against enterococci. | 4 | Stereochemistry |
Owing their large radii, transition metals generally form clusters that are larger than main group elements. One consequence of their increased size, these clusters often contain atoms at their centers. A prominent example is [FeC(CO)]. In such cases, the rules of electron counting assume that the interstitial atom contributes all valence electrons to cluster bonding. In this way, [FeC(CO)] is equivalent to [Fe(CO)] or [Fe(CO)]. | 7 | Physical Chemistry |
Diazirines have been used in photoaffinity labeling experiments involving nucleic acids as well. Examples include:
* Incorporation of a diazirine moiety on a nucleoside sugar in a DNA polymer to investigate interactions between the minor groove of DNA and DNA polymerases.
* Incorporation of a diazirine moiety on a nucleoside base in a DNA polymer to investigate the mode of DNA repair by proteins.
Diazirines have also been used to study protein lipid interactions, for example the interaction of various sphingolipids with proteins in vivo. | 5 | Photochemistry |
Tactoids are liquid crystal microdomains nucleated in isotropic phases, which can be distinguished as spherical or spindle-shaped birefringent microdroplets under polarized light microscopy. Tactoids are a transition state between isotropic and macroscopic liquid crystalline phases. The first observation of tactoids was made by Zocher in 1925, when he studied the nematic phase formed in vanadium pentoxide sols. After that, tactoids have been found in the phase transition processes in many lyotropic liquid crystalline substances, such as tobacco mosaic virus, polypeptides, and cellulose nanocrystals. | 1 | Biochemistry |
An organotroph is an organism that obtains hydrogen or electrons from organic substrates. This term is used in microbiology to classify and describe organisms based on how they obtain electrons for their respiration processes. Some organotrophs such as animals and many bacteria, are also heterotrophs. Organotrophs can be either anaerobic or aerobic.
Antonym: Lithotroph, Adjective: Organotrophic. | 1 | Biochemistry |
Optical waveguide lightmode spectroscopy (OWLS) is a device that relies on a thin-film optical waveguide, enclosing a discrete number of guided electromagnetic waves. Guidance is achieved by means of a grating coupler. It is based on the measurements of effective refractive index of a thin-film layer above the waveguide. This technique works only on highly transparent surfaces.
Other methods widely used for measuring the amount of protein adsorbed on surfaces include radio-labelling, Lowry assay, scanning angle reflectometry, total internal reflection fluorescence, bicinchoninic acid assay etc. | 1 | Biochemistry |
Unlike the hydrogens on the carbon vertices, the hydrogens on the boron vertices are not acidic and do not react with strong bases. This is because boron is not as electronegative as carbon and thus the polarity of the B—H bonds is relatively low. Substitution at the boron vertices is still possible using halogenating agents through electrophilic substitution or photochemical reactions.
For example, the boron vertices at the 9 and 12 positions opposite to the carbon vertices can be iodinated using iodine and a catalytic amount of AlCl while in refluxing dichloromethane.
Exohedral halogenation leads to an increase in the electron withdrawing effect of the carborane which increases the acidity of the C—H bonds especially when the halogens are located at the 9, and 12 positions. Per-halogenation is also possible and when increasing the number of halide atoms, the π backdonation ability of the halide decreases allowing for the formation of intramolecular halide-halide noncovalent bonds.
Iodinated derivatives of carborane can be further modified to access boron alkylated products via a cross coupling reaction. This can be done by treating the halogenated carborane with a Grignard reagent in the presence of a phosphine palladium complex. The bromo and chloro compounds do not react under the same conditions. | 7 | Physical Chemistry |
The main source of atmospheric free oxygen is photosynthesis, which produces sugars and free oxygen from carbon dioxide and water:
Photosynthesizing organisms include the plant life of the land areas, as well as the phytoplankton of the oceans. The tiny marine cyanobacterium Prochlorococcus was discovered in 1986 and accounts for up to half of the photosynthesis of the open oceans. | 5 | Photochemistry |
The identification of one or more key bond disconnections may lead to the identification of key substructures or difficult to identify rearrangement transformations in order to identify the key structures.
* Disconnections that preserve ring structures are encouraged.
* Disconnections that create rings larger than 7 members are discouraged.
*Disconnection involves creativity. | 0 | Organic Chemistry |
The definition of a coil coating process according to EN 10169:2010 is a ‘process in which an (organic) coating material is applied on rolled metal strip in a continuous process which includes cleaning, if necessary, and chemical pre-treatment of the metal surface and either one-side or two-side, single or multiple application of (liquid) paints or coating powders which are subsequently cured or/and laminating with permanent plastic films’.
The metal substrate (steel or aluminum) is delivered in coil form from the rolling mills. Coil weights vary from 5-6 tons for aluminum and up to about 25 tons for steel. The coil is positioned at the beginning of the line, then unwound at a constant speed, passing through the various pre-treatment and coating processes before being recoiled. Two strip accumulators at the beginning and the end of the line enable the work to be continuous, allowing new coils to be added (and finished coils removed) by a metal stitching process without slowing down or stopping the line. | 8 | Metallurgy |
1,1,2,2-Tetrafluoroethane (also called R-134 or HFC-134) is a hydrofluorocarbon, a fluorinated alkane. It is an isomer of the more-used 1,1,1,2-tetrafluoroethane (R-134a). It is used as a foam expansion agent and heat transfer fluid. | 2 | Environmental Chemistry |
Structures built of concrete and reinforced with metal rebar are also subject to damage by oxide jacking. Expansion of corroded rebar causes spalling of the concrete. Structures exposed to a marine environment, or where salt is used for de-icing purposes, are especially susceptible to this type of damage. This may also be caused by concrete having been installed without sufficient cover for the rebars, allowing moisture to reach the metal and cause oxidation.
Research in the 1960s showed that 22 percent of concrete bridge decks in Pennsylvania showed signs of spalling due to oxide jacking within four years of construction. Oxide jacking caused widespread damage to concrete council houses built in the United Kingdom in the post World War II era.
According to an expert in the field, the problem resulted in "intensive worldwide research into the causes and repair of reinforcement corrosion, which in turn led to a vast output of research papers, conferences and publications on the subject." | 8 | Metallurgy |
Some experimental work towards developing quantum computers use trapped ions. Units of quantum information called qubits are stored in stable electronic states of each ion, and quantum information can be processed and transferred through the collective quantized motion of the ions, interacting by the Coulomb force. Lasers are applied to induce coupling between the qubit states (for single qubit operations) or between the internal qubit states and external motional states (for entanglement between qubits). | 7 | Physical Chemistry |
Natural iron ores are mixtures of iron and unwanted impurities, or gangue. In ancient times, these impurities were removed by slagging. Slag was removed by liquation, that is, solid gangue was converted into a liquid slag. The temperature of the process was high enough for the slag to exist in its liquid form.
Smelting was conducted in various types of furnaces. Examples are the bloomery furnace and the blast furnace. The condition in the furnace determines the morphology, chemical composition and the microstructure of the slag.
The bloomery furnace produced iron in a solid state. This is because the bloomery process was conducted at a temperature lower than the melting point of iron metal. Carbon monoxide from the incomplete combustion of charcoal slowly diffused through the hot iron oxide ore, converting it to iron metal and carbon dioxide.
Blast furnaces were used to produce liquid iron. The blast furnace was operated at higher temperatures and at a greater reducing condition than the bloomery furnace. A greater reducing environment was achieved by increasing the fuel to ore ratio. More carbon reacted with the ore and produced a cast iron rather than solid iron. Also, the slag produced was less rich in iron.
A different process was used to make "tapped" slag. Here, only charcoal was added to the furnace. It reacted with oxygen, and generated carbon monoxide, which reduced the iron ore to iron metal. The liquefied slag separated from the ore, and was removed through the tapping arch of the furnace wall.
In addition, the flux (purifying agent), the charcoal ash and the furnace lining contributed to the composition of the slag.
Slag may also form during smithing and refining. The product of the bloomery process is heterogeneous blooms of entrapped slag. Smithing is necessary to cut up and remove the trapped slag by reheating, softening the slag and then squeezing it out. On the other hand, refining is needed for the cast iron produced in the blast furnace. By re-melting the cast iron in an open hearth, the carbon is oxidized and removed from the iron. Liquid slag is formed and removed in this process. | 8 | Metallurgy |
The vibrational spectroscopy methods used to analyze the end groups of a polymer are infrared (IR) and Raman spectroscopy. These methods are useful in fact that the polymers do not need to be soluble in a solvent and spectra can be obtained simply from solid material. A disadvantage of the technique is that only qualitative data is typically obtained on the identification end groups. | 7 | Physical Chemistry |
Reactive compatibilization is a procedure in which immiscible polymer blends are compatibilized by creating copolymers in the solution or melt state. Copolymers are formed when the proper functional groups in each component of the immiscible blend interact in the compatibilization process. These interactions include hydrogen, ionic or covalent bonding. The functional groups that cause these interactions can be the end groups that are already present in the blend polymers (e.g., carboxylic acids or alcohols on polyesters, or amine groups on nylons). Another approach is to add functional groups to the component chains by grafting. The many possible functional groups allow for many types of commercial polymer blends, including polyamide/polyalkene blend systems.
There are a number of advantages reactive compatibilization has over using the traditional block or graft copolymer as the compatibilizing agent. Unlike the latter approach, reactive compatibilization does not rely on diffusing pre-formed copolymers. Copolymers form at the interfaces of the two immiscible blends and do not need to be dispersed. In the traditional approach the system needs to be well mixed when adding the copolymers. Reactive compatibilization is also much more efficient than traditional compatibilization. This is because in reactive compatibilization, functional groups are either already present, or easily grafted on the blend components. In the traditional compatibilization, copolymers must be synthesized on a case-by-case basis for the components to blend. | 7 | Physical Chemistry |
Van de Flierdt is interested in the marine-terminating sector of the East Antarctic Ice Sheet during past warm periods. Her research looks to develop new geochemical and isotopic tracers in marine geochemistry, paleoceanography and paleoclimate, with particular focus on radiogenic isotopes. She is co-lead of the MAGIC Isotope group in the Department of Earth Sciences at Imperial College London. She is also a research at the Lamont–Doherty Earth Observatory at Columbia University.
She is part of the international Geotraces program. Part of the Geotraces program is to ensure results for trace elements and isotopes collected on different cruises by different laboratories can be compared in a meaningful way. Van de Flierdt is building a global database of neodymium in the oceans and researching the implications for paleoceanography research.
In 2012 she won a Leverhulme Trust grant to research deep sea corals. She was part of the Natural Environment Research Council project SWEET, Super-Warm Early Eocene Temperatures and climate. She has led several major NERC grants, totalling well over a £1,000,000 as principal investigator. Van de Flierdt is a member of the Royal Societys International Exchange Committee. She is an editor of Geochimica et Cosmochimica Acta. She has appeared on the podcast Forecast: Climate Conversations'. | 9 | Geochemistry |
Non-linear inverse Compton scattering is an interesting phenomenon for all applications requiring high-energy photons since NICS is capable of producing photons with energy comparable to and higher. In the case of electrons, this means that it is possible to produce photons with MeV energy that can consequently trigger other phenomena such as pair production, Breit–Wheeler pair production, Compton scattering, nuclear reactions.
In the context of laser-plasma acceleration, both relativistic electrons and laser pulses of ultra-high intensity can be present, setting favourable conditions for the observation and the exploitation of non-linear inverse Compton scattering for high-energy photon production, for diagnostic of electron motion, and for probing non-linear quantum effects and non-linear QED. Because of this reason, several numerical tools have been introduced to study non-linear inverse Compton scattering. For example, particle-in-cell codes for the study of laser-plasma acceleration have been developed with the capabilities of simulating non-linear inverse Compton scattering with Monte Carlo methods. These tools are used to explore the different regimes of NICS in the context of laser-plasma interaction. | 7 | Physical Chemistry |
Dextrorphan was under development for the treatment of stroke, and reached phase II clinical trials for this indication, but development was discontinued. | 4 | Stereochemistry |
A pH indicator is a halochromic chemical compound added in small amounts to a solution so the pH (acidity or basicity) of the solution can be determined visually or spectroscopically by changes in absorption and/or emission properties. Hence, a pH indicator is a chemical detector for hydronium ions (HO) or hydrogen ions (H) in the Arrhenius model.
Normally, the indicator causes the color of the solution to change depending on the pH. Indicators can also show change in other physical properties; for example, olfactory indicators show change in their odor. The pH value of a neutral solution is 7.0 at 25°C (standard laboratory conditions). Solutions with a pH value below 7.0 are considered acidic and solutions with pH value above 7.0 are basic. Since most naturally occurring organic compounds are weak electrolytes, such as carboxylic acids and amines, pH indicators find many applications in biology and analytical chemistry. Moreover, pH indicators form one of the three main types of indicator compounds used in chemical analysis. For the quantitative analysis of metal cations, the use of complexometric indicators is preferred, whereas the third compound class, the redox indicators, are used in redox titrations (titrations involving one or more redox reactions as the basis of chemical analysis). | 7 | Physical Chemistry |
Tritium was released to the atmosphere during atmospheric testing of nuclear bombs. Radioactive decay of tritium produces the noble gas helium-3. Comparing the ratio of tritium to helium-3 (H/He) allows estimation of the age of recent ground waters. A small amount of tritium is also produced naturally by cosmic ray spallation and spontaneous ternary fission in natural uranium and thorium, but due to the relatively short half-life of tritium and the relatively small quantities (compared to those from anthropogenic sources) those sources of tritium usually play only a secondary role in the analysis of groundwater.
* [http://water.usgs.gov/lab/3h3he/background/ USGS Tritium/Helium-3 Dating]
* [http://wwwrcamnl.wr.usgs.gov/isoig/period/he_iig.html Hydrologic Isotope Tracers - Helium] | 9 | Geochemistry |
A surrogate to BOD has been developed using a resazurin derivative which reveals the extent of oxygen uptake by micro-organisms for organic matter mineralization. A cross-validation performed on 109 samples in Europe and the United-States showed a strict statistical equivalence between results from both methods.
An electrode has been developed based on the luminescence emission of a photo-active chemical compound and the quenching of that emission by oxygen. This quenching photophysics mechanism is described by the Stern–Volmer equation for dissolved oxygen in a solution:
* : Luminescence in the presence of oxygen
* : Luminescence in the absence of oxygen
* : Stern-Volmer constant for oxygen quenching
* : Dissolved oxygen concentration
The determination of oxygen concentration by luminescence quenching has a linear response over a broad range of oxygen concentrations and has excellent accuracy and reproducibility. | 3 | Analytical Chemistry |
Duplornaviricota contains most dsRNA viruses, including reoviruses, which infect a diverse range of eukaryotes, and cystoviruses, which are the only dsRNA viruses known to infect prokaryotes. Apart from RdRp, viruses in Duplornaviricota also share icosahedral capsids that contain 60 homo- or heterodimers of the capsid protein organized on a pseudo T=2 lattice. The phylum is divided into three classes: Chrymotiviricetes, which primarily contains fungal and protozoan viruses, Resentoviricetes, which contains reoviruses, and Vidaverviricetes, which contains cystoviruses. | 1 | Biochemistry |
The possible increased effect a pulsed current will have on the corrodibility of metals was first looked at by de la Rive in 1837. It was investigated around 60 years later by Coehn regarding the effect of a current with a rectangular waveform, on the plating of zinc deposits, resulting in a successful application for a patent. A full review on using PDC electrolysis in electroplating, also known as electrodeposition or pulse plating, was only published in 1954 by Baeyens, this being the first area of research into the use of pulse electrolysis in industry.
A pulsed current can be varied in many ways that increases the possible outcomes and can vary the properties of deposited metals during electroplating. Hansel and Roy, in their review of the third European Pulse Plating Seminar, concluded that each deposition system must have a unique sequence developed in order to optimise the process and gain the desired results, opposing the inability of traditional plating to be as freely tailored to a situation. The nucleation and crystallisation of the deposition metal is directly affected and can have favourable or unfavourable circumstances if specific conditions are not met. It is reported that pulse plating can encourage nucleation causing grain refinement, and reducing grain size, as well as increasing the deposit density that can improve micro hardness.
These effects were first researched on zinc by Coehn. It was discovered a pulsed current at a high frequency can produce deposits of higher quality, with properties ranging from a smoother finish by the reduction in grain size, as well as lowering its corrosion rate. This is beneficial as it is mainly used as a sacrificial anode in industry. | 7 | Physical Chemistry |
The polyprismanes consist of multiple prismanes stacked base-to-base. The carbons at each intermediate level—the n-gon bases where the prismanes fuse to each other—have no hydrogen atoms attached to them. | 4 | Stereochemistry |
The csiD promoter (csiD) is essential for the expression of csiD(carbon starvation induced gene), ygaF and the gab genes. The csiD is activated exclusively under carbon starvation conditions and stationary phase during which cAMP accumulates in high concentrations in the cell. The binding of cAMP to the cAMP receptor protein(CRP) causes CRP to bind tightly to a specific DNA site in the csiD promoter, thus activating the transcription of genes downstream of the promoter.
The gabD exerts an additional control over the gabDTP region. The gabD is activated by σ inducing conditions such as hyperosmotic and acidic shifts besides starvation and stationary phase. The gabD promoter on the other hand, is σ dependent and is activated under nitrogen limitation. In nitrogen limiting conditions, the nitrogen regulator Nac binds to a site located just upstream of the promoter expressing the gab genes. The gab genes upon activation produce enzymes that degrade GABA to succinate. | 1 | Biochemistry |
A mirror image (in a plane mirror) is a reflected duplication of an object that appears almost identical, but is reversed in the direction perpendicular to the mirror surface. As an optical effect it results from reflection off from substances such as a mirror or water. It is also a concept in geometry and can be used as a conceptualization process for 3-D structures. | 4 | Stereochemistry |
Historically, the theory was used to model nonuniform adsorbates and multi-components solutes. For certain pairs of adsorbates and adsorbents, the mathematical parameters of the Polyani theory can be related to the physicochemical properties of both adsorbents and adsorbates. The theory has been used to model the adsorption of carbon nanotubes and carbon nanoparticles. In the study done by Yang and Xing, the theory have been shown to better fit the adsorption isotherm than Langmuir, Freundlich, and partition. The experiment studied the adsorption of organic molecules on carbon nanoparticles and carbon nanotubes. According to the Polyani theory the surface defect curvatures of carbon nanoparticles could affect their adsorption. Flat surfaces on the particles will allow more surface atoms to approach adsorbing organic molecules which will increase the potential, leading to stronger interactions. The theory has been beneficial in trying to understand the adsorption mechanisms of organic compounds on carbon nanoparticles and estimating the adsorption capacity and affinity. Using this theory, researchers are hoping to be able to design carbon nanoparticles for specific needs such as using them as sorbents in environmental studies. | 7 | Physical Chemistry |
Because retroviruses are able to recombine with each other and with other endogenous DNA sequences, it would be beneficial for gene therapy to explore the potential risks HERVs can cause, if any. Also, this ability of HERVs to recombine can be manipulated for site-directed integration by including HERV sequences in retroviral vectors. | 1 | Biochemistry |
A prototypical spatio-spectral scanning system, introduced in June 2014, consists of a basic slit spectroscope (slit + dispersive element) at some suitable, non-zero distance before a camera. (If the effective camera distance is zero, the system is applicable to spatial scanning). The imaging process is based on spectrally-decoded camera obscura projections: A series of projections from a continuous array of pinholes (= the slit) is projected onto the dispersive element, each projection contributing a rainbow-colored strip to the recorded two-dimensional image. The field of view in the wavelength-coded spatial dimension asymptotically approaches the dispersion angle of the dispersive element as the camera distance from the dispersive element approaches infinity.
Scanning is achieved by moving the camera transverse to the slit (stationary platform), or by moving the entire system transverse to the slit (mobile platform). | 7 | Physical Chemistry |
Besides the introduction of mutations, Overlap Extension PCR is widely used to assemble complex DNA sequences without the introduction of undesired nucleotides at any position. This is possible since OE-PCR relies on the utilization of complementary overhangs to guide the scarless splicing of custom DNA fragments in a desired order. This is the main advantage of OE-PCR and other long-homology based cloning methos such as Gibson assembly, which overcome the limitations of traditional restriction enzyme digestion and ligation cloning methods.
Assembly of custom DNA sequences with OE-PCR consists on three main steps. First, individual DNA sequences are amplified by PCR from different templates and flanked with the required complementary overhangs. Second, the formerly obtained PCR products are combined together into the overlap extension PCR reaction, where the complementary overhangs bind pair-wise allowing the polymerase to extend the DNA strand. Eventually, outer primers targeting the external overhangs are used and the desired DNA product is amplified in the final PCR reaction. | 1 | Biochemistry |
Rolling hairpin replication (RHR) is a unidirectional, strand displacement form of DNA replication used by parvoviruses, a group of viruses that constitute the family Parvoviridae. Parvoviruses have linear, single-stranded DNA (ssDNA) genomes in which the coding portion of the genome is flanked by telomeres at each end that form hairpin loops. During RHR, these hairpin loops repeatedly unfold and refold to change the direction of DNA replication so that replication progresses in a continuous manner back and forth across the genome. RHR is initiated and terminated by an endonuclease encoded by parvoviruses that is variously called NS1 or Rep, and RHR is similar to rolling circle replication, which is used by ssDNA viruses that have circular genomes.
Before RHR begins, a host cell DNA polymerase converts the genome to a duplex form in which the coding portion is double-stranded and connected to the terminal hairpins. From there, messenger RNA (mRNA) that encodes the viral initiator protein is transcribed and translated to synthesize the protein. The initiator protein commences RHR by binding to and nicking the genome in a region adjacent to a hairpin called the origin and establishing a replication fork with its helicase activity. Nicking leads to the hairpin unfolding into a linear, extended form. The telomere is then replicated and both strands of the telomere refold back in on themselves to their original turn-around forms. This repositions the replication fork to switch templates to the other strand and move in the opposite direction. Upon reaching the other end, the same process of unfolding, replication, and refolding occurs.
Parvoviruses vary in whether both hairpins are the same or different. Homotelomeric parvoviruses such as adeno-associated viruses (AAV), i.e. those that have identical or similar telomeres, have both ends replicated by terminal resolution, the previously described process. Heterotelomeric parvoviruses such as minute virus of mice (MVM), i.e. those that have different telomeres, have one end replicated by terminal resolution and the other by an asymmetric process called junction resolution. During asymmetric junction resolution, the duplex extended form of the telomere reorganizes into a cruciform-shaped junction, and the correct orientation of the telomere is replicated off the lower arm of the cruciform. As a result of RHR, a replicative molecule that contains numerous copies of the genomes is synthesized. The initiator protein periodically excises progeny ssDNA genomes from this replicative concatemer. | 1 | Biochemistry |
In chemistry, a thiyl radical has the formula RS, sometimes written RS to emphasize that they are free radicals. R is typically an alkyl or aryl substituent. Because S–H bonds are about 20% weaker than C–H bonds, thiyl radicals are relatively easily generated from thiols RSH. Thiyl radicals are intermediates in the thiol-ene reaction, which is the basis of some polymeric coatings and adhesives. They are generated by hydrogen-atom abstraction from thiols using initiators such as AIBN:
:RN=NR → 2 R + N
:R + R′SH → R′S + RH
Thiyl radicals are also invoked as intermediates in some biochemical reactions. | 0 | Organic Chemistry |
*[https://research.bidmc.org/ncfg National Center for Functional Glycomics (NCFG)] The focus of the NCFG is the development in the glycosciences, with an emphasis on exploring the molecular mechanisms of glycan recognition by proteins important in human biology and disease. They have a number of [https://ncfg.hms.harvard.edu/resources resources for glycan analysis] as well as [https://ncfg.hms.harvard.edu/training training in glycomics] and [https://ncfg.hms.harvard.edu/protocols protocols for glycan analysis]
* [https://glytoucan.org/ GlyTouCan], Glycan structure repository
* [http://glycosciences.de/ Glycosciences.DE], German glycan database
* [http://glycoscience.ru Carbohydrate Structure Database], Russian glycan database
* [http://unicarbkb.org UniCarbKB], Australian glycan database
* [https://web.archive.org/web/20130703194144/http://glycosuitedb.expasy.org/glycosuite/glycodb GlycoSuiteDB], glycan database by Swiss Institute of Bioinformatics
* [https://www.glygen.org/ GlyGen], NIH funded glycoinformatics resource
* The Consortium for Functional Glycomics (CFG) is a non-profit research initiative comprising eight core facilities and 500+ [http://www.functionalglycomics.org/glycomics/common/jsp/useraccess/pipeople.jsp participating investigators] that work together to develop [http://www.functionalglycomics.org/static/consortium/resources.shtml resources and services] and make them available to the scientific community free of charge. The data generated by these resources are captured in databases accessible through the [http://www.functionalglycomics.org Functional Glycomics Gateway], a web resource maintained through a partnership between the CFG and Nature Publishing Group.
* [http://dels.nas.edu/Report/Transforming-Glycoscience-Roadmap/13446 Transforming Glycoscience: A Roadmap for the Future] by the U.S. National Research Council. This site provides information about the U.S. National Research Council's reports and workshops on glycoscience. | 0 | Organic Chemistry |
Formation of the Pol I preinitiation complex requires the binding of selective factor 1 (SL1 or TIF-IB) to the core element of the rDNA promoter. SL1 is a complex composed of TBP and at least three TBP-associated factors (TAFs). For basal levels of transcription, only SL1 and the initiation-competent form of Pol I (Pol Iβ), characterized by RRN3 binding, are required.
For activated transcription levels, UBTF (UBF) is also required. UBTF binds as a dimer to both the upstream control element (UCE) and core element of the rDNA promoter, bending the DNA to form an enhanceosome. SL1 has been found to stabilize the binding of UBTF to the rDNA promoter.
The subunits of the Pol I PIC differ between organisms. | 1 | Biochemistry |
Materials with broad absorption bands are being applied in pigments, dyes and optical filters. Titanium dioxide, zinc oxide and chromophores are applied as UV absorbers and reflectors in sunscreen. | 7 | Physical Chemistry |
TOXMAP helped users create nationwide, regional, or local area maps showing where TRI chemicals are released on-site into the air, water, ground, and by underground injection, as reported by industrial facilities in the United States. It also identified the releasing facilities, color-codes release amounts for a single year or year range, and provides multi-year aggregate chemical release data and trends over time, starting with 1988. Maps also can show locations of Superfund sites on the Agency for Toxic Substances and Disease Registry National Priorities List (NPL), which lists all chemical contaminants present at these sites. TOXMAP is a useful environmental health tool that makes epidemiological and environmental information available to the public.
There were two versions of TOXMAP available from its home page: the classic version of TOXMAP released in 2004 and, a newer version released in 2014 that is based on Adobe Flash/Apache Flex technology. In addition to many of the features of TOXMAP classic, the new version provides an improved map appearance and interactive capabilities as well as a more current GIS look-and-feel. This included seamless panning, immediate update of search results when zooming to a location, two collapsible side panels to maximize map size, and automatic size adjustment after a window resize. The new TOXMAP also improved U.S. Census layers and availability by Census Tract (2000 and 2010), Canadian National Pollutant Release Inventory (NPRI) data, U.S. commercial nuclear power plants, as well as improved and updated congressional district boundaries.
TOXMAP classic users may search the system by location (such as city, state, or ZIP code), chemical name, chemical name fragment, release medium, release amount, facility name and ID, and can filter results to those residing within a pre-defined or custom geographic region.
Search results may be brought up in Google Maps or Google Earth, or saved for use in other tools. TOXMAP also overlays map data such as U.S. Census population information, income figures from the Bureau of Economic Analysis, and health data from the National Cancer Institute and the National Center for Health Statistics.
The data shown in TOXMAP comes from the following sources:
* EPA Toxics Release Inventory (TRI)
* EPA Superfund Program (National Priorities List/NPL)
* Environment Canada
* National Institute of Environmental Health Sciences (NIEHS) Superfund Research Program
* Hazardous Substances Data Bank
* [https://www.nlm.nih.gov/pubs/factsheets/toxlinfs.html NLM TOXLINE (Toxicology Bibliographic Information)]
* Agency for Toxic Substances and Disease Registry
* National Atlas of the United States
* Surveillance, Epidemiology, and End Results database
* National Center for Health Statistics
* Nuclear Regulatory Commission
* Esri | 1 | Biochemistry |
Eukaryotic initiation factor 4F (eIF4F) is a heterotrimeric protein complex that binds the 5' cap of messenger RNAs (mRNAs) to promote eukaryotic translation initiation. The eIF4F complex is composed of three non-identical subunits: the DEAD-box RNA helicase eIF4A, the cap-binding protein eIF4E, and the large "scaffold" protein eIF4G. The mammalian eIF4F complex was first described in 1983, and has been a major area of study into the molecular mechanisms of cap-dependent translation initiation ever since. | 1 | Biochemistry |
* Mercury(I) chloride disproportionates upon UV-irradiation:
* Phosphorous acid disproportionates upon heating to 200°C to give phosphoric acid and phosphine:
* Desymmetrizing reactions are sometimes referred to as disproportionation, as illustrated by the thermal degradation of bicarbonate:
:: The oxidation numbers remain constant in this acid-base reaction.
* Another variant on disproportionation is radical disproportionation, in which two radicals form an alkene and an alkane.
* Disproportionation of sulfur intermediates by microorganisms are widely observed in sediments.
* Chlorine gas reacts with dilute sodium hydroxide to form sodium chloride, sodium chlorate and water. The ionic equation for this reaction is as follows:
:: The chlorine reactant is in oxidation state 0. In the products, the chlorine in the Cl ion has an oxidation number of −1, having been reduced, whereas the oxidation number of the chlorine in the ClO ion is +5, indicating that it has been oxidized.
* Decomposition of numerous interhalogen compounds involve disproportionation. Bromine fluoride undergoes disproportionation reaction to form bromine trifluoride and bromine in non-aqueous media:
* The dismutation of superoxide free radical to hydrogen peroxide and oxygen, catalysed in living systems by the enzyme superoxide dismutase:
:: The oxidation state of oxygen is −1/2 in the superoxide free radical anion, −1 in hydrogen peroxide and 0 in dioxygen.
* In the Cannizzaro reaction, an aldehyde is converted into an alcohol and a carboxylic acid. In the related Tishchenko reaction, the organic redox reaction product is the corresponding ester. In the Kornblum–DeLaMare rearrangement, a peroxide is converted to a ketone and an alcohol.
* The disproportionation of hydrogen peroxide into water and oxygen catalysed by either potassium iodide or the enzyme catalase:
* In the Boudouard reaction, carbon monoxide disproportionates to carbon and carbon dioxide. The reaction is for example used in the HiPco method for producing carbon nanotubes, high-pressure carbon monoxide disproportionates when catalysed on the surface of an iron particle:
* Nitrogen has oxidation state +4 in nitrogen dioxide, but when this compound reacts with water, it forms both nitric acid and nitrous acid, where nitrogen has oxidation states +5 and +3 respectively:
* Dithionite undergoes acid hydrolysis to thiosulfate and bisulfite:
* Dithionite also undergoes alkaline hydrolysis to sulfite and sulfide:
* Dithionate is prepared on a larger scale by oxidizing a cooled aqueous solution of sulfur dioxide with manganese dioxide: | 0 | Organic Chemistry |
P680 is the strongest biological oxidizing agent known, with an estimated redox potential of ~1.3 V. This makes it possible to oxidize water during oxygenic photosynthesis. P680 recovers its lost electron by oxidizing water via the oxygen-evolving complex, which regenerates P680. | 5 | Photochemistry |
From their earliest days both Fulmer and Yarsley Testing Laboratories had carried out a wide variety of tests for clients and had designed and constructed specialized test equipment. In 1982 both Fulmer Technical Services and Yarsley Technical Centre were awarded accreditation from the National Testing Laboratory Accreditation Scheme (NATLAS).
By the late 1970s American and European governments and business leaders had become increasingly concerned about competition from Japan. Many decided to adopt some Japanese industrial practices, including quality management, which was thought to have played a large part in the Japanese economic miracle. Beginning in the early 1980s, the quality standard BS 5750 (1979) became widely adopted by British companies. In 1985, Yarsley Technical Centre, which already had a strong background in standards and accreditation, established Yarsley Quality Assured Firms (YQAF) as an independent certification body, supported by the UK Department of Trade and Industry. YQAF assessed conformity to BS 5750 and certified conforming companies. Its certification service was overseen by an independent Certification Board under an independent chairman, thus ensuring that there was no conflict of interest with YQAF's consultancy services.
YQAF was successful and grew rapidly by establishing a network of regional offices throughout the UK. It was incorporated in 1987 and gained accreditation from the National Accreditation Council for Certification Bodies (NACCB). | 8 | Metallurgy |
Unlike neutral homoaromatic compounds, anionic homoaromatics are widely accepted to exhibit "true" homoaromaticity. These anionic compounds are often prepared from their neutral parent compounds through lithium metal reduction. 1,2-diboretanide derivatives show strong homoaromatic character through their three-atom (boron, boron, carbon), two-electron bond, which contains shorter C-B bonds than in the neutral classical analogue. These 1,2-diboretanides can be expanded to larger ring sizes with different substituents and all contain some degree of homoaromaticity.
Anionic homoaromaticity can also be seen in dianionic bis-diazene compounds, which contain a four-atom (four nitrogens), six-electron center. Experiment results have shown the shortening of the transannular nitrogen-nitrogen distance, therefore demonstrating that dianionic bis-diazene is a type of anionic bishomoaromatic compound. Peculiar feature of these systems is that the cyclic electron delocalization is taking place in the σ-plane defined by the four nitrogens. These bis-diazene-dianions are therefore the first examples for 4-center-6-electron σ-bishomoaromaticity. The corresponding 2 electron σ-bishomoaromatic systems were realized in the form of pagodane dications (see above). | 7 | Physical Chemistry |
Specialized manufacturing is required for the electrodes, and details of their design and construction are typically trade secrets. However, with purchase of suitable electrodes, a standard multimeter can be used to complete the construction of the pH meter. However, commercial suppliers offer voltmeter displays that simplify use, including calibration and temperature compensation. | 7 | Physical Chemistry |
The first synthetic porphyrin isomer was reported by Emanual Vogel and coworkers in 1986. This isomer [18]porphyrin-(2.0.2.0) is named as porphycene, and the central N Cavity forms a rectangle shape as shown in figure. Porphycenes showed interesting photophysical behavior and found versatile compound towards the photodynamic therapy. This inspired Vogel and Sessler to took up the challenge of preparing [18]porphyrin-(2.1.0.1) and named it as corrphycene or porphycerin. The third porphyrin that is [18]porphyrin-(2.1.1.0), was reported by Callot and Vogel-Sessler. Vogel and coworkers reported successful isolation of [18]porphyrin-(3.0.1.0) or isoporphycene. The Japanese scientist Furuta and Polish scientist Latos-Grażyński almost simultaneously reported the N-confused porphyrins. The inversion of one of the pyrrolic subunits in the macrocyclic ring resulted in one of the nitrogen atoms facing outwards from the core of the macrocycle. | 1 | Biochemistry |
Room-temperature ionic liquids (RTILs) are dominated by salts derived from 1-methylimidazole, i.e., 1-alkyl-3-methylimidazolium. Examples include 1-ethyl-3-methyl- (EMIM), 1-butyl-3-methyl- (BMIM), 1-octyl-3 methyl (OMIM), 1-decyl-3-methyl-(DMIM), 1-dodecyl-3-methyl- (dodecylMIM). Other imidazolium cations are 1-butyl-2,3-dimethylimidazolium (BMMIM or DBMIM) and 1,3-di(N,N-dimethylaminoethyl)-2-methylimidazolium (DAMI). Other N-heterocyclic cations are derived from pyridine: 4-methyl-N-butyl-pyridinium (MBPy) and N-octylpyridinium (C8Py). Conventional quaternary ammonium cations also form ILs, e.g. tetraethylammonium (TEA) and tetrabutylammonium (TBA). | 7 | Physical Chemistry |
Similar N-glycan biosynthesis pathway have been found in prokaryotes and Archaea. However, compared to eukaryotes, the final glycan structure in eubacteria and archaea does not seem to differ much from the initial precursor made in the endoplasmic reticulum. In eukaryotes, the original precursor oligosaccharide is extensively modified en route to the cell surface. | 0 | Organic Chemistry |
In canonical notch signaling, ligand proteins bind to the extracellular domain of the notch receptor and induce the cleavage and release of the intracellular domain into the cytoplasm. This subsequently interacts with other proteins, enters the nucleus, and regulates gene expression.
In 2006, a non-canonical branch of the notch signaling pathway was discovered. Using cultures of mouse neural stem cells, notch activation was shown to lead to the phosphorylation of several kinases (PI3K, Akt, mTOR) and subsequent phosphorylation of the serine residue of STAT3 in the absence of any detectable phosphorylation of the tyrosine residue of STAT3, a modification that is widely studied in the context of cancer biology. Following this event, Hes3 mRNA was elevated within 30 minutes. Subsequently, the consequences of this pathway were studied. | 1 | Biochemistry |
A polyprotic acid is a compound which may lose more than 1 proton. Stepwise dissociation constants are each defined for the loss of a single proton. The constant for dissociation of the first proton may be denoted as K and the constants for dissociation of successive protons as K, etc. Phosphoric acid, , is an example of a polyprotic acid as it can lose three protons.
When the difference between successive pK values is about four or more, as in this example, each species may be considered as an acid in its own right; In fact salts of may be crystallised from solution by adjustment of pH to about 5.5 and salts of may be crystallised from solution by adjustment of pH to about 10. The species distribution diagram shows that the concentrations of the two ions are maximum at pH 5.5 and 10.
When the difference between successive pK values is less than about four there is overlap between the pH range of existence of the species in equilibrium. The smaller the difference, the more the overlap. The case of citric acid is shown at the right; solutions of citric acid are buffered over the whole range of pH 2.5 to 7.5.
According to Paulings first rule, successive pK values of a given acid increase . For oxyacids with more than one ionizable hydrogen on the same atom, the pK' values often increase by about 5 units for each proton removed, as in the example of phosphoric acid above.
It can be seen in the table above that the second proton is removed from a negatively charged species. Since the proton carries a positive charge extra work is needed to remove it, which is why pK is greater than pK. pK is greater than pK because there is further charge separation. When an exception to Pauling's rule is found, it indicates that a major change in structure is also occurring. In the case of (aq), the vanadium is octahedral, 6-coordinate, whereas vanadic acid is tetrahedral, 4-coordinate. This means that four "particles" are released with the first dissociation, but only two "particles" are released with the other dissociations, resulting in a much greater entropy contribution to the standard Gibbs free energy change for the first reaction than for the others. | 7 | Physical Chemistry |
Hammonds postulate is useful for understanding the relationship between the rate of a reaction and the stability of the products. While the rate of a reaction depends just on the activation energy (often represented in organic chemistry as ΔG “delta G double dagger”), the final ratios of products in chemical equilibrium depends only on the standard free-energy change ΔG (“delta G'”). The ratio of the final products at equilibrium corresponds directly with the stability of those products.
Hammond's postulate connects the rate of a reaction process with the structural features of those states that form part of it, by saying that the molecular reorganizations have to be small in those steps that involve two states that are very close in energy. This gave birth to the structural comparison between the starting materials, products, and the possible "stable intermediates" that led to the understanding that the most stable product is not always the one that is favored in a reaction process. | 7 | Physical Chemistry |
The double helix is an important tertiary structure in nucleic acid molecules which is intimately connected with the molecule's secondary structure. A double helix is formed by regions of many consecutive base pairs.
The nucleic acid double helix is a spiral polymer, usually right-handed, containing two nucleotide strands which base pair together. A single turn of the helix constitutes about ten nucleotides, and contains a major groove and minor groove, the major groove being wider than the minor groove. Given the difference in widths of the major groove and minor groove, many proteins which bind to DNA do so through the wider major groove. Many double-helical forms are possible; for DNA the three biologically relevant forms are A-DNA, B-DNA, and Z-DNA, while RNA double helices have structures similar to the A form of DNA. | 4 | Stereochemistry |
Weatherization (American English) or weatherproofing (British English) is the practice of protecting a building and its interior from the elements, particularly from sunlight, precipitation, and wind, and of modifying a building to reduce energy consumption and optimize energy efficiency.
Weatherization is distinct from building insulation, although building insulation requires weatherization for proper functioning. Many types of insulation can be thought of as weatherization, because they block drafts or protect from cold winds. Whereas insulation primarily reduces conductive heat flow, weatherization primarily reduces convective heat flow.
In the United States, buildings use one third of all energy consumed and two thirds of all electricity. Due to the high energy usage, they are a major source of the pollution that causes urban air quality problems and pollutants that contribute to climate change. Building energy usage accounts for 49 percent of sulfur dioxide emissions, 25 percent of nitrous oxide emissions, and 10 percent of particulate emissions. | 7 | Physical Chemistry |
Stereocenters can exist on chiral or achiral molecules. They are defined as a location (point) within a molecule, rather than a particular atom, in which the interchanging of two groups creates a stereoisomer. A stereocenter can have either four different attachment groups, or three different attachment groups where one group is connected by a double bond. Since stereocenters can exist on achiral molecules, stereocenters can have either sp or sp hybridization. | 4 | Stereochemistry |
The procedure begins by making a cell lysate of the cells of interest. This lysate contains polysomes, monosomes (composed of one ribosome residing on an mRNA), the small (40S in eukaryotes) and large (60S in eukaryotes) ribosomal subunits, "free" mRNA and a host of other soluble cellular components.
The procedure continues by making a continuous sucrose gradient of continuously variable density in a centrifuge tube. At the concentrations used (15-45% in the example), sucrose does not disrupt the association of ribosomes and mRNA. The 15% portion of the gradient is at the top of the tube, while the 45% portion is at the bottom because of their different density.
A specific amount (as measured by optical density) of the lysate is then layered gently on top of the gradient in the tube. The lysate, even though it contains a large amount of soluble material, is much less dense than 15% sucrose, and so it can be kept as a separate layer at the top of the tube if this is done gently.
In order to separate the components of the lysate, the preparation is subjected to centrifugation. This accelerates the components of the lysate with many times the force of gravity and thus propels them through the gradient based upon how "big" the individual components are. The small (40S) subunits travel less far into the gradient than the large (60S) subunits. The 80S ribosomes on an mRNA travel further (note that the contribution of the size of the mRNA to the distance traveled is not significant). Polysomes composed of 2 ribosomes travel further, polysomes with 3 ribosomes travel further still, and on and on. The "size" of the components is designated by S, the svedberg unit. Note that one S = 10 seconds, and that the concept of "big" is actually an oversimplification.
After centrifugation, the contents of the tube are collected as fractions from the top (smaller, slower traveling) to bottom (bigger, faster traveling) and the optical density of the fractions is determined. The first fractions removed have a large amount of relatively small molecules, such as tRNAs, individual proteins, etc. | 1 | Biochemistry |
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